Modern processes of lacustrine plant sedimentary ancient DNA

doi:10.17521/cjpe.2021.0386

Abstract

Abstract:

Study on paleovegetation is with great significance on understanding the modern vegetation composition, distribution, and its responses to global change. During recent decades, it has been a rapidly developing field in molecular palaeoecology to track the long-term vegetation composition and plant diversity changes by using sedimentary ancient DNA. Meanwhile, the lacustrine sedimentary ancient plant DNA (PsedaDNA) is becoming a popular proxy for palaeovegetation and palaeoecological studies. However, the modern process of PsedaDNA remains unclear compared with pollen analysis, which limits its further application. Here, we reviewed the PsedaDNA researches and tried to elucidate the modern processes of PsedaDNA, including the source, deposition, and preservation processes, and to understand the relationships between the PsedaDNA and modern vegetation. PsedaDNA is mainly derived from the lake surroundings or within the catchment. The abundance and composition of PsedaDNA are influenced by the biomass of terrestrial plants, and factors such as DNA degradation, the adsorption, and dilution of particles in soils and sediments during the transportation and deposition. Moreover, the preservation of PsedaDNA is largely affected by both biotic and abiotic factors, including the microbial activity, chemical properties of lake water (conductivity and pH), and sediment composition. PsedaDNA can be used to reveal the contemporary vegetation and climate information but was incompetent to quantitatively palaeovegetation reconstruction. Considering the complexity of modern processes, the interpretation of PsedaDNA results should be done with extra caution. To sum up, PsedaDNA is still in its infancy, which has been benefiting from the progress of molecular biotechnology, optimization of experimental design, species barcodes, and sophistication of reference databases. The PsedaDNA technique including DNA metabarcoding and metagenomics will certainly promote the development of Chinese palaeophytoecology research.

Key words: lake sedimentation, ancient plant DNA, taphonomy, vegetation representativeness, palaeovegetation, palaeoecology

WU Kai, LI Kai, JIA Wei-Han, LIAO Meng-Na, NI Jian. Modern processes of lacustrine plant sedimentary ancient DNA[J]. Chin J Plant Ecol, 2022, 46(7): 735-752.

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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2021.0386

https://www.plant-ecology.com/EN/Y2022/V46/I7/735

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序号 Serial number	研究地点 Study site	材料来源 Source materials	研究方法 Methodology	物种检测率 Species detection rate			DNA结果分辨率 DNA resolution				参考文献 Reference
序号 Serial number	研究地点 Study site	材料来源 Source materials	研究方法 Methodology	花粉 Pollen	大化石 Macrofossil	DNA	目 Order	科 Family	属 Genus	种 Species	参考文献 Reference
1	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	20	16					Parducci et al., 2012
2	挪威瑞典边界 Norwegian-Swedish border	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	46	-	14					Parducci et al., 2013
3	格陵兰 Greenland	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	46	37	13					Pedersen et al., 2013
4	非洲 Africa	泥炭、湖泊沉积物 Peat, Lacustrine sediments	宏条形码 Metabarcoding	26	-	34					Boessenkool et al., 2014
5	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	90	-	14					Paus et al., 2015
6	芬兰、俄罗斯西北部 Finland, Northwest Russian	泥炭 Peat	宏条形码 Metabarcoding	54	36	10					Parducci et al., 2015
7	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	30	34		13	32	19	Alsos et al., 2016
8	格陵兰 Greenland	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	17	1	2	7	7	Epp et al., 2015
9	阿尔卑斯山 Alps	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	43		30	38	9	Pansu et al., 2015
10	阿尔卑斯山 Alps	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	43		30	38	9	Pansu et al., 2015	白令海峡 Bering Strait	湖泊沉积物 Lacustrine sediments	宏基因组学 Metagenomics	32	18	40	Pedersen et al., 2016
11	白令海峡 Bering Strait	湖泊沉积物 Lacustrine sediments	宏基因组学 Metagenomics	64	22	55					Pedersen et al., 2016
12	非洲 Africa	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	>100	-	42		22	21		Bremond et al., 2017
13	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	43	-	114		12	50	52	Niemeyer et al., 2017
14	苏格兰 Scotland	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	73					Sjögren et al., 2017
15	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	84	-	113	1	22	49	40	Zimmermann et al., 2017
16	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	81					Alsos et al., 2018
17	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	39	-	118		14	55	49	Clarke et al., 2019a
18	瑞典 Sweden	泥炭 Peat	宏基因组学 Metagenomics	44	22	51	13	11	16	11	Parducci et al., 2019
19	极地乌拉尔 Polar Urals	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	115	-	134		20	60	54	Clarke et al., 2019b, 2020
20	非洲乌干达 Uganda, Africa	泥炭 Peat	宏基因组学 Metagenomics	-	-	21					Dommain et al., 2020
21	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	52	-	120				42	Liu et al., 2020
22	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	59	-	117				45	Liu et al., 2020
23	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	55	-	90				34	Liu et al., 2020

序号 Serial number	研究地点 Study site	材料来源 Source materials	研究方法 Methodology	物种检测率 Species detection rate			DNA结果分辨率 DNA resolution				参考文献 Reference
序号 Serial number	研究地点 Study site	材料来源 Source materials	研究方法 Methodology	花粉 Pollen	大化石 Macrofossil	DNA	目 Order	科 Family	属 Genus	种 Species	参考文献 Reference
1	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	20	16					Parducci et al., 2012
2	挪威瑞典边界 Norwegian-Swedish border	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	46	-	14					Parducci et al., 2013
3	格陵兰 Greenland	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	46	37	13					Pedersen et al., 2013
4	非洲 Africa	泥炭、湖泊沉积物 Peat, Lacustrine sediments	宏条形码 Metabarcoding	26	-	34					Boessenkool et al., 2014
5	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	90	-	14					Paus et al., 2015
6	芬兰、俄罗斯西北部 Finland, Northwest Russian	泥炭 Peat	宏条形码 Metabarcoding	54	36	10					Parducci et al., 2015
7	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	30	34		13	32	19	Alsos et al., 2016
8	格陵兰 Greenland	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	17	1	2	7	7	Epp et al., 2015
9	阿尔卑斯山 Alps	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	43		30	38	9	Pansu et al., 2015
10	阿尔卑斯山 Alps	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	43		30	38	9	Pansu et al., 2015	白令海峡 Bering Strait	湖泊沉积物 Lacustrine sediments	宏基因组学 Metagenomics	32	18	40	Pedersen et al., 2016
11	白令海峡 Bering Strait	湖泊沉积物 Lacustrine sediments	宏基因组学 Metagenomics	64	22	55					Pedersen et al., 2016
12	非洲 Africa	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	>100	-	42		22	21		Bremond et al., 2017
13	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	43	-	114		12	50	52	Niemeyer et al., 2017
14	苏格兰 Scotland	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	73					Sjögren et al., 2017
15	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	84	-	113	1	22	49	40	Zimmermann et al., 2017
16	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	-	-	81					Alsos et al., 2018
17	挪威 Norway	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	39	-	118		14	55	49	Clarke et al., 2019a
18	瑞典 Sweden	泥炭 Peat	宏基因组学 Metagenomics	44	22	51	13	11	16	11	Parducci et al., 2019
19	极地乌拉尔 Polar Urals	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	115	-	134		20	60	54	Clarke et al., 2019b, 2020
20	非洲乌干达 Uganda, Africa	泥炭 Peat	宏基因组学 Metagenomics	-	-	21					Dommain et al., 2020
21	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	52	-	120				42	Liu et al., 2020
22	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	59	-	117				45	Liu et al., 2020
23	西伯利亚 Siberia	湖泊沉积物 Lacustrine sediments	宏条形码 Metabarcoding	55	-	90				34	Liu et al., 2020

	对比方面 Contrast aspect	花粉 Pollen	植物古DNA Plant ancient DNA
现代过程 Modern process	产率 Productivity	已有相对花粉产率研究, 花粉R值 Relative pollen productivity and R-value	-
	来源范围 Source area	区域尺度 Regional-scale	流域尺度、湖泊周边 Catchment scale and around the lake
	传播途径 Dispersal route	风力传播为主, 兼有流水搬运、昆虫携带和坡面侵蚀等 Anemophilous, water transportation, entomophilous, and slope erosion pathway	风力传播较弱, 流水搬运更强, 兼有昆虫携带和坡面侵蚀等 Weaker anemophilous, stronger water transportation, entomophilous and slope erosion pathway
	损伤机制 Damage mechanism	机械破碎和化学溶蚀 Mechanical disruption and chemical corrosion	普遍发生的DNA降解, 如脱嘌呤作用、水解作用和氧化作用以及微生物分解 Common DNA degradation, such as depurination, hydrolysis, oxidation and microbial decomposition
	致损原因 Cause of damage	仅在部分特殊环境下才导致花粉严重损伤, 如高pH或强水动力条件 Only in some special conditions, such as high pH or strong hydrodynamic conditions	紫外线、pH、微生物、温度、水分等 UV, pH, microorganisms, temperature, moisture, etc
	埋藏后过程 Post burial process	表层扰动 Surface disturbance	表层扰动、DNA降解 Surface disturbance, DNA degradation
	埋藏时间 Burial time	第四纪甚至更久 ≥Quaternary	小于10万年 <100 000 years
与现代植被的关系 Relationship with modern vegetation	物种分辨率 Species resolution	科、属, 部分到种 Family, genus, partly to species	科、属、种、亚种 Family, genus, species, subspecies
	植物代表性 Plant representativeness	花粉R值等 Pollen R-value, etc	仅部分结果支持DNA丰度与现代植被丰度正相关 Only a few results support the positive correlation
	重建古植被 Palaeovegetation reconstruction	BIOME和REVEALS模型等 BIOME and REVEALS model etc	-
	植物多样性研究 Relevant studies	花粉多样性和植被多样性 Pollen diversity and vegetation diversity	植物多样性, 能够揭示更多的稀有种或本地种 Plant diversity, reveal more rare or native species
其他 Else	研究过程 Research process	依赖分类专家, 鉴定结果耗时较长 Needs taxonomists and takes a long time	依赖实验操作流程的质量控制, 包括污染控制、数据真实性验证等; 依赖现代植物分子数据库 Not only relies on the operation quality control, including pollution control and data authenticity verification but also needs the modern plant molecular database
其他 Else	应用 Application	局地或区域植物群落变化, 植被类型变化; 标准化, 可进行远距离的研究结果对比, 已用于探讨大尺度的植被演变、古气候变化等科学问题 Changes of local or regional plant communities and vegetation types. Standardization can be used to compare different research results and has been used to discuss large-scale vegetation evolution, palaeoclimate change, and other scientific problems	植物物种发育关系, 局地植物群落变化, 植被类型和植物多样性变化; 方法个性化导致不同研究结果无法直接对比, 或者存在较大的不确定性 Phylogenetic relationships of plant species, changes of local plant communities, vegetation types, and plant diversity. The individuation of methods leads to the inability of direct comparison between different research results, or the existence of great uncertainty

	对比方面 Contrast aspect	花粉 Pollen	植物古DNA Plant ancient DNA
现代过程 Modern process	产率 Productivity	已有相对花粉产率研究, 花粉R值 Relative pollen productivity and R-value	-
	来源范围 Source area	区域尺度 Regional-scale	流域尺度、湖泊周边 Catchment scale and around the lake
	传播途径 Dispersal route	风力传播为主, 兼有流水搬运、昆虫携带和坡面侵蚀等 Anemophilous, water transportation, entomophilous, and slope erosion pathway	风力传播较弱, 流水搬运更强, 兼有昆虫携带和坡面侵蚀等 Weaker anemophilous, stronger water transportation, entomophilous and slope erosion pathway
	损伤机制 Damage mechanism	机械破碎和化学溶蚀 Mechanical disruption and chemical corrosion	普遍发生的DNA降解, 如脱嘌呤作用、水解作用和氧化作用以及微生物分解 Common DNA degradation, such as depurination, hydrolysis, oxidation and microbial decomposition
	致损原因 Cause of damage	仅在部分特殊环境下才导致花粉严重损伤, 如高pH或强水动力条件 Only in some special conditions, such as high pH or strong hydrodynamic conditions	紫外线、pH、微生物、温度、水分等 UV, pH, microorganisms, temperature, moisture, etc
	埋藏后过程 Post burial process	表层扰动 Surface disturbance	表层扰动、DNA降解 Surface disturbance, DNA degradation
	埋藏时间 Burial time	第四纪甚至更久 ≥Quaternary	小于10万年 <100 000 years
与现代植被的关系 Relationship with modern vegetation	物种分辨率 Species resolution	科、属, 部分到种 Family, genus, partly to species	科、属、种、亚种 Family, genus, species, subspecies
	植物代表性 Plant representativeness	花粉R值等 Pollen R-value, etc	仅部分结果支持DNA丰度与现代植被丰度正相关 Only a few results support the positive correlation
	重建古植被 Palaeovegetation reconstruction	BIOME和REVEALS模型等 BIOME and REVEALS model etc	-
	植物多样性研究 Relevant studies	花粉多样性和植被多样性 Pollen diversity and vegetation diversity	植物多样性, 能够揭示更多的稀有种或本地种 Plant diversity, reveal more rare or native species
其他 Else	研究过程 Research process	依赖分类专家, 鉴定结果耗时较长 Needs taxonomists and takes a long time	依赖实验操作流程的质量控制, 包括污染控制、数据真实性验证等; 依赖现代植物分子数据库 Not only relies on the operation quality control, including pollution control and data authenticity verification but also needs the modern plant molecular database
其他 Else	应用 Application	局地或区域植物群落变化, 植被类型变化; 标准化, 可进行远距离的研究结果对比, 已用于探讨大尺度的植被演变、古气候变化等科学问题 Changes of local or regional plant communities and vegetation types. Standardization can be used to compare different research results and has been used to discuss large-scale vegetation evolution, palaeoclimate change, and other scientific problems	植物物种发育关系, 局地植物群落变化, 植被类型和植物多样性变化; 方法个性化导致不同研究结果无法直接对比, 或者存在较大的不确定性 Phylogenetic relationships of plant species, changes of local plant communities, vegetation types, and plant diversity. The individuation of methods leads to the inability of direct comparison between different research results, or the existence of great uncertainty